My altitude above sea level is 400 meters. This is a relatively low point in my area. The 300 meter wind level of the map is 100 meters underground, Yet, there is a wind field for that altitude, and it's different from the surface field!

I have the same question that rjeff already asked a while ago (but which I didn't find to be answered, yet):
In case of e.g. wind, what does the height mean exactly. I understood that ground level means 10m above ground and other heights use sea level as reference.
But:
What if I am looking for wind data in the mountains? In that case you also provide wind data for e.g. 100m (above sea level) which is below the ground.
I feel, as long as surface height is not reached, there should be empty spots on the map.

@Hecky 100m layer is also above ground level (above model terrain), it is the same case like 10m level.
Upper layers display values for isobaric surfaces, e.g. 850hPa, not for exact altitude. AMSL value in the tooltip is only approximation.

Still not clear -- So do you mean that when I have "1000 meters" selected for wind altitude, that when I'm looking at an area that is 1,500 meters MSL, the wind strength indication is for 1050 meters MSL in that particular point? (And then it goes to 1000 meters where the terrain slopes below that level?)

Q: What exactly does “surface” mean in this particular case?
A: surface means the model's surface that is the average elevation of an area 9x9 km (for ECMWF model) around your location. If the area is smooth, the model's orography is very close to reality. Over mountainous areas the situation is more complex.
Because valleys and mountain peaks are smoothed out by the model orography the direct model output of 10m wind (or 2 m temperature) may represent an altitude significantly different from the real one.

Q: And if the elevation of the terrain in the surrounding area is 3000ft (therefore 5200ft AMSL) are we getting their respective “surface” data?
A: Probably yes. It would be nice if we could know the "reference altitude" for a location (as we know the reference coordinates).

Q: But most important, what does it mean if I choose 330ft or 2000ft charts in these particular examples?
A: You'll have almost the same readout as for surface.

@pa58am
Wind gust represents a maximum since the previous post-processing.
Thus, gust valid on certain time represents the max. wind during the previous
forecast period (3 hrs for ECMWF).
Example: gust value at 6 o'clock represents max. wind during the period from 3 to 6 o'clock.

For your 2nd question (why it is sometimes less than wind speed?)
please send a screenshot.